Plants are constantly challenged by a wide variety of pathogenic organisms including viruses, bacteria, fungi, and nematodes. Crop plants are particularly vulnerable because they are usually grown as genetically uniform monocultures; when disease strikes, losses can be severe. However, most plants have their own innate mechanisms of defense against pathogenic organisms. Natural disease resistance genes often provide high levels of resistance to or immunity against pathogens.
Systemic acquired resistance (SAR) is one component of the complex system plants use to defend themselves from pathogens (Hunt and Ryals, Crit. Rev. in Plant Sci. 15, 583-606 (1996); Ryals et al., Plant Cell 8, 1809-1819 (1996); and U.S. Pat. No. 5,614,395; each of which is incorporated herein by reference). SAR is a particularly important aspect of plant-pathogen responses because it is a pathogen-inducible, systemic resistance against a broad spectrum of infectious agents, including viruses, bacteria, and fungi. When the SAR signal transduction pathway is blocked, plants become more susceptible to pathogens that normally cause disease, and they also become susceptible to some infectious agents that would not normally cause disease (Gaffney et al., Science 261, 754-756 (1993); Delaney et al., Science 266, 1247-1250 (1994); Delaney et al., Proc. Natl. Acad. Sci. USA 92, 6602-6606 (1995); Delaney, Plant Phys. 113, 5-12 (1997); Bi et al., Plant J. 8, 235-245 (1995); and Mauch-Mani and Slusarenko, Plant Cell 8, 203-212 (1996); each of which is incorporated herein by reference). These observations indicate that the SAR signal transduction pathway is critical for maintaining plant health.
Conceptually, the SAR response can be divided into two phases. In the initiation phase, a pathogen infection is recognized and a signal is released that travels through the phloem to distant tissues. This systemic signal is perceived by target cells, which react by expression of both SAR genes and disease resistance. The maintenance phase of SAR refers to the period of time, from weeks up to the entire life of the plant, during which the plant is in a quasi steady state and disease resistance is maintained (Ryals et al., 1996).
Associated with the onset of SAR is the expression of a set of genes called SAR genes, many of which belong to the family of pathogenesis-related (PR) proteins. A protein is classified as an SAR protein when its presence or activity correlates tightly with maintenance of SAR (Neuenschwander et al., Plant-Microbe Interactions, Vol. 1, G. Stacey & N. T. Keen, eds. (New York, N.Y.: Chapman and Hall), pp. 81-106 (1996), incorporated herein by reference). These proteins represent markers for SAR in a sense that SAR is not found in the absence of SAR proteins. PR proteins are induced in large amounts in response to infection by various pathogens, including viruses, bacteria and fungi. Some of these proteins have a role in providing systemic acquired resistance to the plant. Pathogenesis-related proteins were first discovered in tobacco plants (Nicotiana tabacum) reacting hypersensitively to infection with tobacco mosaic virus (TMV). Subsequently, PR proteins have been found in many plant species (See, for example, Redolfi et al. (1983) Neth J Plant Pathol 89:245-254; Van Loon (1985) Plant Mol. Biol. 4:111-116; and Uknes et al. (1992) Plant Cell 4:645-656; all of which are incorporated herein by reference.) Such proteins are believed to be a common defensive systemic response of plants to infection by pathogens. Pathogenesis-related proteins include, but are not limited to, SAR8.2 proteins, acidic and basic forms of tobacco PR-1a, PR-1b, and PR-1c, PR-1', PR-2, PR-2', PR-2", PR-N, PR-O, PR-O', PR-4, PR-P, PR-Q, PR-S, and PR-R proteins, cucumber peroxidases, the chitinase which is a basic counterpart of PR-P or PR-Q, and the beta-1,3-glucanase (glucan endo-1,3-beta-glucosidase, EC 3.2.1.39) which is a basic counterpart of PR-2, PR-N or PR-O, and the pathogen-inducible chitinase from cucumber. See, for example, Ward et al. (1991) Plant Cell 3, 1085-1094, incorporated herein by reference. See also, Uknes et al. (1992); and U.S. Pat. No. 5,614,395. Transgenic disease-resistant plants have been created by transforming plants with various SAR genes, including PR protein genes (U.S. Pat. No. 5,614,395).
Salicylic acid (SA) accumulation appears to be required for SAR signal transduction. Plants that cannot accumulate SA due to treatment with specific inhibitors, epigenetic repression of phenylalanine ammonia-lyase, or transgenic expression of salicylate hydroxylase, which specifically degrades SA, also cannot exhibit either SAR gene expression or disease resistance (Gaffney et al., 1993; Delaney et al., 1994; Mauch-Mani and Slusarenko 1996; Maher et al., Proc. Natl. Acad. Sci. USA 91, 7802-7806 (1994), incorporated herein by reference; Pallas et al., Plant J. 10, 281-293 (1996), incorporated herein by reference). Although it has been suggested that SA might serve as the systemic signal, this is currently controversial and, to date, all that is known for certain is that if SA cannot accumulate, then SAR signal transduction is blocked (Pallas et al., 1996; Shulaev et al., Plant Cell 7, 1691-1701 (1995), incorporated herein by reference; Vernooij et al., Plant Cell 6, 959-965 (1994), incorporated herein by reference).
Recently, Arabidopsis has emerged as a model system to study SAR (Uknes et al. (1992); Uknes et al., Mol. Plant-Microbe Interact. 6, 692-698 (1993); Cameron et al., Plant J. 5, 715-725 (1994); Mauch-Mani and Slusarenko, Mol. Plant-Microbe Interact. 7, 378-383 (1994); Dempsey and Klessig, Bulletin de L'Institut Pasteur 93, 167-186 (1995); all of which are incorporated herein by reference). It has been demonstrated that SAR can be activated in Arabidopsis by both pathogens and chemicals, such as SA, 2,6-dichloroisonicotinic acid (INA) and benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester (BTH) (Uknes et al., 1992; Vernooij et al., Mol. Plant-Microbe Interact. 8, 228-234 (1995), incorporated herein by reference; Lawton et al., Plant J. 10, 71-82 (1996), incorporated herein by reference). Following treatment with either INA or BTH or pathogen infection, at least three PR protein genes, namely, PR-1, PR-2, and PR-5 are coordinately induced concomitant with the onset of resistance (Uknes et al., 1992, 1993).
While there have therefore been advances in plant genetic engineering, the prospects for the general use of these techniques for plant improvement are tempered by the realization that relatively few genes corresponding to plant traits of interest have been identified or cloned. Further, traits of interest often involve multi-gene families. Selection for plants carrying pathogen or disease resistance genes is thus laborious and time consuming. There is therefore needed a method to identify plants expressing resistance genes for use in plant breeding programs.